Impact of normalization and filtering on linkage analysis of gene expression data

Using the Problem 1 data set made available for Genetic Analysis Workshop 15, we assessed sensitivity of linkage results to a correlation-based feature extraction method as well as to different normalization procedures applied to the raw Affymetrix gene expression microarray data. The impact of these procedures on heritability estimates and on expression quantitative trait loci are investigated. The filtering algorithm we propose in this paper ranks genes based on the total absolute correlation of each gene with all other genes on the array and has the potential to extract features that may play role in functional pathways and gene networks. Our results showed that the normalization and filtering algorithms can have a profound influence on genetic analysis of gene expression data.